PDBsum entry 3d24

Transcription

PDB id: 3d24

Contents

Protein chains

209 a.a. *

13 a.a. *

14 a.a. *

Waters ×272

* Residue conservation analysis

PDB id:

3d24

Name:

Transcription

Title:

Crystal structure of ligand-binding domain of estrogen-related receptor alpha (erralpha) in complex with the peroxisome proliferators-activated receptor coactivator-1alpha box3 peptide (pgc-1alpha)

Structure:

Steroid hormone receptor err1. Chain: a, c. Fragment: ligand binding domain: residues 278-519. Synonym: estrogen-related receptor alpha, err-alpha, estrogen receptor-like 1, nuclear receptor subfamily 3 group b member 1. Engineered: yes. Peroxisome proliferator-activated receptor gamma coactivator 1-alpha. Chain: b, d.

Source:

Homo sapiens. Organism_taxid: 9606. Gene: esrra, err1, esrl1, nr3b1. Expressed in: escherichia coli. Synthetic: yes. Other_details: synthetic peptide with the sequence based on the fragment (residues 198-219) of human pgc-1-alpha, uniprot entry q9ubk2 (prgc1_human)

Resolution:

2.11Å R-factor: 0.212 R-free: 0.255

Authors:

D.Moras,H.Greschik,R.Flaig,Y.Sato,N.Rochel,Structural Proteomics In Europe (Spine)

Key ref:

H.Greschik et al. (2008). Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop. J Biol Chem, 283, 20220-20230. PubMed id: 18441008 DOI: 10.1074/jbc.M801920200

Date:

07-May-08 Release date: 10-Jun-08

Protein chains

P11474  (ERR1_HUMAN) -  Steroid hormone receptor ERR1 from Homo sapiens

Seq: 423 a.a.

Struc: 209 a.a.

Protein chain

Q9UBK2  (PRGC1_HUMAN) -  Peroxisome proliferator-activated receptor gamma coactivator 1-alpha from Homo sapiens

Seq: 798 a.a.

Struc: 13 a.a.

Protein chain

Q9UBK2  (PRGC1_HUMAN) -  Peroxisome proliferator-activated receptor gamma coactivator 1-alpha from Homo sapiens

Seq: 798 a.a.

Struc: 14 a.a.

DOI no: 10.1074/jbc.M801920200

J Biol Chem 283:20220-20230 (2008)

PubMed id: 18441008

Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop.

H.Greschik, M.Althage, R.Flaig, Y.Sato, V.Chavant, C.Peluso-Iltis, L.Choulier, P.Cronet, N.Rochel, R.Schüle, P.E.Strömstedt, D.Moras.

ABSTRACT

Although structural studies on the ligand-binding domain (LBD) have established the general mode of nuclear receptor (NR)/coactivator interaction, determinants of binding specificity are only partially understood. The LBD of estrogen receptor-alpha (ERalpha), for example, interacts only with a region of peroxisome proliferator-activated receptor coactivator (PGC)-1alpha, which contains the canonical LXXLL motif (NR box2), whereas the LBD of estrogen-related receptor-alpha (ERRalpha) also binds efficiently an untypical, LXXYL-containing region (NR box3) of PGC-1alpha. Surprisingly, in a previous structural study, the ERalpha LBD has been observed to bind NR box3 of transcriptional intermediary factor (TIF)-2 untypically via LXXYL, whereas the ERRalpha LBD binds this region of TIF-2 only poorly. Here we present a new crystal structure of the ERRalpha LBD in complex with a PGC-1alpha box3 peptide. In this structure, residues N-terminal of the PGC-1alpha LXXYL motif formed contacts with helix 4, the loop connecting helices 8 and 9, and with the C terminus of the ERRalpha LBD. Interaction studies using wild-type and mutant PGC-1alpha and ERRalpha showed that these contacts are functionally relevant and are required for efficient ERRalpha/PGC-1alpha interaction. Furthermore, a structure comparison between ERRalpha and ERalpha and mutation analyses provided evidence that the helix 8-9 loop, which differs significantly in both nuclear receptors, is a major determinant of coactivator binding specificity. Finally, our results revealed that in ERRalpha the helix 8-9 loop allosterically links the LBD homodimer interface with the coactivator cleft, thus providing a plausible explanation for distinct PGC-1alpha binding to ERRalpha monomers and homodimers.

Selected figure(s)

Figure 1.
FIGURE 1. Interaction of CoA peptides with the ERR and the ER LBD. Representations complexed with a PGC-1 box3 peptide (^198QQQKPQRRPCSELLKYLTTNDD^219)(A), the ERR LBD (subunit C)·PGC-1 box 3 complex contoured in electron density at 1 (B), the published ERR LBD (PDB ID: 1XB7 [PDB] ) in complex with a mutant PGC-1 box3 peptide (^205RPASELLKYLTT^216; C207A) (C), and the published ER LBD (PDB ID: 1GWR [PDB] ) co-crystallized with a TIF-2 box3 peptide (^740KENALLRYLLDKDD^753)(D). In all three cases the CoA peptide binds in the untypical LXXYL mode (probably representing a crystal artifact in the case of the ER ·TIF-2 complex). In A and B, residues of PGC-1 that N-terminally flank the LXXYL helix (Arg-205, Pro-206, and Cys-207) interact with the ERR surface, notably with H4, the H8–H9 loop, and the C terminus. In comparison, N-terminal flanking residues are not observed in C and D. In all structures, the length of H12 and the conformation of the C-terminal residues differ.

Figure 5.
FIGURE 5. The H8–H9 loop region contributes to PGC-1 binding selectivity. A, amino acid sequence alignment of selected parts of the ERR and the ER LBD. Residues involved in CoA binding are colored blue; amino acids that differ between the CoA cleft of ERR and ER are underlined. Regions that differ significantly between the two receptors (H8–H9 loop and C terminus) and that have been exchanged in the respective swap mutants are colored red. B, superimposition of the CoA cleft and the H8–H9 loop region of ERR and ER (PDP ID: 1QKU). H9 is longer in ER , and the H8–H9 loop adopts a different conformation. Only selected residues that have been mutated are depicted. C, superimposition of the H8–H9 loop region of ER with the corresponding part of ERR (molecule coloring as in B). The representation illustrates that swapping of the H8–H9 loop of ER into ERR perturbs the homodimer interface and requires conformational adaptations of side chains, mainly because of the presence of the bulky Tyr-459. D, ER mutants probing the contribution of residues to PGC-1 binding (E2, estradiol). In ER (V376M-E380Q), residues that differ in the CoA of ER and ERR have been exchanged. In ER (SwapH8–H9), the H8–H9 loop region (amino acids 457–468) has been replaced with the corresponding region (amino acids 338–341) of ERR . ER (3mut) corresponds to V376M-E380Q-SwapH8–H9-H373S-H377S. In ER (4mut), His-547—Arg-548 of ER have, in addition, been replaced with Met-421—Met-422—Asp-423 of ERR . Mammalian two-hybrid interaction assays were done in BHK cells using Gal4[(5)]-TATA-LUC, pCMX-Gal4-PGC-1 constructs, and wild-type or mutant pCMX-VP16-ERR LBD. Normalized luciferase activity observed with Gal4-PGC-1 ID and VP16-ERR LBD served as the reference and was set to 100%. Bars represent the mean ± S.D. (n 6). p values were calculated for ERR mutants relative to the corresponding values of wild-type ERR (^**, p 0.0001; ^*, p 0.001).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 20220-20230) copyright 2008.

Figures were selected by an automated process.